Dr Nick Thomson


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Bacterial Genomics and Metagenomics


I am interested in using genetic engineering to push the boundaries of what bacteria are able to do, improving upon processes that they naturally possess and engineering new capabilities that are not found in nature.

I did my PhD at the University of Cambridge, working on the production of a type of biodegradable plastic called poly(hydroxybutyrate) by bacteria. As well as looking at ways to improve the yield of production from bacteria, I also improved the production and purification of the key enzyme in the process (PhaC), making it easier both to study the mechanism of the polymerization reaction and to produce poly(hydroxybutyrate) in vitro.

Following my PhD, I won a position as a Foreign Postdoctoral Researcher at RIKEN, Tokyo, Japan. Here, I characterized an E. coli-based ‘cell factory’ in which the cells can be prevented from growing, while remaining metabolically active. This diverts valuable carbon sources away from the wasteful production of more cells and towards the production of the desired product. I measured changes in the concentration of metabolites and proteins in the cells as they entered the non-growing, productive ‘quiescent’ phase. More recently I returned to Cambridge for a proof-of-principle study, in collaboration with the Centre for Process Innovation, to demonstrate that these Q-cells can improve the production efficiency of commodity chemicals at the commercial scale.

My current research focuses on creating ‘smart probiotics’ by attaching functional enzymes to the outer surfaces of bacteria that are able to colonise the gut. These enzymes will add new metabolic capabilities to the bacteria. They will therefore be better able to digest food, compete with pathogens and alter the balance of species inhabiting the gut. In the future, we hope that this will allow us to improve public health (for example, by removing saturated fats before it can be absorbed into the bloodstream), reduce hospital-acquired infections such as MRSA, and fight conditions such as irritable bowel syndrome.

Zhang CZ,Zhang Y,Ding XM,Lin XL,Lian XL,Trampari E,Thomson NM,Ding HZ,Webber MA,Jiang HX. (2020)

Emergence of ciprofloxacin heteroresistance in foodborne Salmonella enterica serovar Agona.

The Journal of antimicrobial chemotherapy

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Foster-Nyarko E,Alikhan NF,Ravi A,Thilliez G,Thomson N,Baker D,Kay G,Antonio M,O J,Pallen MJ. (2020)

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Microbial Genomics, 6

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Thomson NM,Zhang C,Trampari E,Pallen MJ. (2020)

Creation of Golden Gate constructs for Gene Doctoring

BMC Biotechnology

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Holden ER,Wickham GJ,Webber MA,Thomson NM,Trampari E. (2020)

Donor plasmids for phenotypically neutral chromosomal gene insertions in Enterobacteriaceae.

Microbiology (Reading, England)

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Ravi A., Halstead F. D., Bamford A., Casey A., Thomson N. M., van Schaik W., Snelson C., Goulden R., Foster-Nyarko E., Savva G. M., Whitehouse T., Pallen M., Oppenheim B. A.. (2019)

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.

Microbial genomics, Volume 5, Issue 9, 10.1099/mgen.0.000293

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Halstead F. D., Ravi A., Thomson N., Nuur M., Hughes K., Brailey M., Oppenheim B. A.. (2018)

Whole genome sequencing of toxigenic Clostridium difficile in asymptomatic carriers: insights into possible role in transmission.

The Journal of hospital infection

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Thomson N. M., Shirai T., Chiapello M., Kondo A., Mukherjee K. J., Sivaniah E., Numata K., Summers D. K.. (2017)

Efficient 3-Hydroxybutyrate Production by Quiescent Escherichia coli Microbial Cell Factories is Facilitated by Indole-Induced Proteomic and Metabolomic Changes.

Biotechnology Journal, 13, e1700571

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